A cladistic analysis of Siboglinidae Caullery, 1914 (Polychaeta, Annelida): formerly the phyla Pogonophora and Vestimentifera

It has been proposed in recent years that the phyla Pogonophora and Vestimentifera are a derived clade of polychaete annelids. It has also been proposed that if this clade belongs among polychaetes, then the taxon name Pogonophora is misleading and should revert to a name first formulated for the group, Siboglinidae Caullery, 1914. This recommendation is adopted in this paper, and a cladistic study using terminals of 'generic' rank in the former Pogonophora (including Vestimentifera) is undertaken. The purpose of this is to assess which taxon names should now be used for clades within Siboglinidae, and to provide a revised taxonomy, based on phylogenetic principles. Another major aim is to assess the position of the vestimentiferan clade within Siboglinidae. The results show that Vestimentifera is the sister group to Sclerolinum, and this clade is then sister group to Frenulata, i.e. the remaining Siboglinidae. The results suggest that all taxa within Siboglinidae that are not genera or species are redundant, except for the following: Siboglinidae is defined as the first polychaete, and all its descendants, to have an gut occluded by expanded endoderm filled with chemoautotrophic bacteria, as seen in the holotype of Riftia pachyptila Jones, 1981. Monilifera can be defined based on apomorphy-based system such that it is the first siboglinid, and all its descendants, to have rings of chaetae (uncini) in the opisthosoma, as seen in the holotype of Sclerolinum magdalenae Southward, 1972. Vestimentifera can be denned as the first siboglinid and all its descendants to have a vestimentum as seen in the holotype of Riftia pachyptia. Frenulata is defined as the siboglinid, and all its descendants, to have a mid-trunk girdle, as seen in the holotype of Siboglinum weberi Caullery, 1914. The taxa of generic rank are not defined here since their monophyly was not investigated.     

Siboglinid evolution shaped by habitat preference and sulfide tolerance

Siboglinids are tube-dwelling annelids that inhabit marine reducing habitats such as anoxic mud bottoms, seeps and hydrothermal vents. As adults, they lack a functional digestive system and rely on chemoautotrophic microbial endosymbionts. Based on morphological analyses, Siboglinidae form a clade with the Sabellariidae, Serpulidae and Sabellidae within the Annelida. The sister group to this clade is the Oweniidae. Three subgroups constitute the Siboglinidae: Frenulata typically inhabit anoxic sediments, Sclerolinium (a.k.a., Monilifera) live on decaying organic matter or reduced sediments and Vestimentifera are mostly found at hydrocarbon seeps and hydrothermal vents. Recent studies suggest that Sclerolinum is the sister group to the Vestimentifera. Within the Vestimentifera, the species inhabiting bare-rock hydrothermal vents represent a derived clade. The seep-inhabiting genus Lamellibrachia forms a basal branch within the Vestimentifera. Trends in siboglinid evolution are most notable with regard to the level of sulfide tolerance and type of substrate. Basal groups inhabit soft substrate with only slightly elevated sulfide levels, whereas more derived species colonize hard substrate and tolerate elevated temperatures and high levels of sulfide. The type of substrate correlates with tube morphology and the function of the opisthosome. The role of the symbionts in habitat selection needs further investigation.     

The Osedax trophosome: organization and ultrastructure

The polychaete family Siboglinidae, which is currently construed as comprising the Frenulata, Monilifera (composed of Sclerolinum), Vestimentifera, and Osedax, has become known for its specialized symbiont-housing organ called the trophosome. This organ replaced the digestive system of the worms and is located in the elongated trunk region in Frenulata, Sclerolinum, and Vestimentifera. Currently two types of trophosomes have been described: in the taxa Frenulata and Sclerolinum the bacteriocytes originate from endoderm, and in Vestimentifera they originate from mesoderm. In Osedax, a trophosome was described as lacking (Rouse et al., 2004), but bacteriocytes are located in Osedax's characteristic root tissue. Here, we argue for a consistent name for the symbiont-housing tissue, namely trophosome, as in other siboglinids. In this study we provide morphological evidence that in Osedax the bacteriocytes are derived from somatic mesoderm. We show that the trophosome in Osedax is an apolar tissue composed of bacteriocytes and nonsymbiotic cells. As in vestimentiferans, a specific cell cycle was identified; however, in this case it is directed from the posterior to the anterior end of the worms instead of from the center toward the periphery. Comparison of all siboglinid trophosomes and re-evaluation of their body regions allows us to discuss whether the trophosomes are homologous and to hypothesize about the organization of the last common ancestor of Siboglinidae.     

Molecular phylogeny of siboglinid annelids (a.k.a. pogonophorans): a review

Siboglinid, or pogonophoran, annelids are tubicolous worms that rely on chemoautotrophic endosymbionts for nutrition. Three clades within the siboglinids are recognized: Frenulata, Vestimentifera, and Monilifera. As a group, these worms have received considerable attention from molecular phylogenetists. Most studies have focused either on the evolutionary origins of the group or on the relationships within vestimentiferans, which live at hydrocarbon seeps and hydrothermal vents. Here I review the literature to date on siboglinid molecular phylogeny and summarize the clade’s evolution. The vestimentiferans have been well studied, especially in the eastern Pacific. The seep taxon Lamellibrachia is basal in the clade with vent species being more derived. Recent studies of seeps are finding new species and suggest that habitat depth can be correlated with species boundaries. In contrast to the vestimentiferans, frenulate evolution has been poorly studied. Despite their greater apparent diversity, frenulate specimens have not been sampled so extensively, and thus little is known about their evolution. Sclerolinum, also referred to as Monilifera, is a recognized genus of siboglinids that forms the sister group to Vestimentifera. Like the frenulates, little is known about the history of this group. Our present understanding of siboglinid phylogeny has, in large part, been dictated by insufficient sampling effort.     

Spermatozoa and sperm aggregates in the vestimentiferan Lamellibrachia luymesi compared with those of Riftia pachyptila (Polychaeta: Siboglinidae: Vestimentifera)

The spermatozoa and the sperm bundles of the vestimentiferans Riftia pachyptila and Lamellibrachia luymesi (Annelida: Siboglinidae) were studied using several microscopical techniques (transmission and scanning electron microscopy, and confocal microscopy) and compared with some other annelid sperm. The spermatozoa and sperm bundles of both species show a similar structure, but they differ in the dimensions of the components of individual cells and in the number of spermatozoa forming each sperm bundle. The spermatozoa of R. pachyptila and L. luymesi are filiform cells composed, in sequence, by an acrosome in the form of a thread-like helical vesicle, an elongated coiled nucleus surrounded by two helical mitochondria, and a long flagellum. In the spermatozoa of both species, the apical portion of the nucleus is completely devoid of chromatin and is delimited by a thickened nuclear envelope with a fibrillar appearance. Both species have sperm bundles that resemble buds, having a calyx-like portion formed by the helical heads, and a stalk-like portion formed by the tightly packed flagella. A parsimony analysis based on spermatozoal characters showed monophyly of the Siboglinidae and the Vestimentifera. We propose a new set of autapomorphies characterizing vestimentiferan spermatozoa. Our analysis suggests that spermatozoal characters are useful to the understanding of the phylogeny of the group.     

Organization and microanatomy of the Sclerolinum contortum trophosome (Polychaeta, Siboglinidae)

The trophosome-an organ especially evolved to accommodate symbiotic bacteria-is a key character of the polychaete family Siboglinidae. Astonishingly, the trophosomes vary in organization and origin between the different siboglinid taxa. The trophosome of the small genus Sclerolinum was nearly unknown until now. Here we investigated the trophosome of S. contortum from the Gulf of Mexico, using light and electron microscopy. We show that this organ derives from the visceral mesoderm and propose that the trophosome of the sister clade Vestimentifera and Sclerolinum is a homologous character. Like that of juvenile vestimentiferans, the trophosome of Sclerolinum trophosome is simply organized. This study reveals that the Sclerolinum trophosome exhibits two regions that differ in the organization of host tissue and the size and shape of the symbionts. We suggest that a specific cell cycle within the symbiont-housing organ is directed along the longitudinal body axis, with a region of proliferation anteriorly and a region of degradation posteriorly. Using Raman microspectroscopy we demonstrate that the endosymbionts of S. contortum from the Gulf of Mexico contain sulfur vesicles, and we argue for a chemoautotrophic sulfur-oxidizing metabolism.     

Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology

Complete coding regions of the 18S rRNA gene of an enteropneust hemichordate and an echinoid and ophiuroid echinoderm were obtained and aligned with 18S rRNA gene sequences of all major chordate clades and four outgroups. Gene sequences were analyzed to test morphological character phylogenies and to assess the strength of the signal. Maximum- parsimony analysis of the sequences fails to support a monophyletic Chordata; the urochordates form the sister taxon to the hemichordates, and together this clade plus the echinoderms forms the sister taxon to the cephalochordates plus craniates. Decay, bootstrap, and tree-length distribution analyses suggest that the signal for inference of dueterostome phylogeny is weak in this molecule. Parsimony analysis of morphological plus molecular characters supports both monophyly of echinoderms plus enteropneust hemichordates and a sister group relationship of this clade to chordates. Evolutionary parsimony does not support chordate monophyly. Neighbor-joining, Fitch-Margoliash, and maximum-likelihood analyses support a chordate lineage that is the sister group to an echinoderm-plus-hemichordate lineage. The results illustrate both the limitations of the 18S rRNA molecule alone for high- level phylogeny inference and the importance of considering both molecular and morphological data in phylogeny reconstruction.      

Review and preliminary phylogenetic analysis of the subfamilies of the Pyralidae (sensu stricto) (Lepidoptera: Pyraloidea)

Abstract. The morphological evidence on the monophyly of the subfamilies of the Pyralidae sensu stricto is reviewed, and a phylogeny is proposed for the Pyralidae. New autapomorphies are proposed for the monophyly of the Phycitinae, Pyralinae and Epipaschiinae. The phylogenetic analysis supports a sister group relationship between the Phycitinae and Epipaschiinae, a sister group relationship of the Pyralinae to the phycitine + epipaschiine clade. The galleriines and chrysaugines occupy basally unresolved positions.     

Molecular characterization of bacteria associated with the trophosome and the tube of Lamellibrachia sp., a siboglinid annelid from cold seeps in the eastern Mediterranean

Specimens of Lamellibrachia ( Annelida: Siboglinidae ) were recently discovered at cold seeps in the eastern Mediterranean. In this study, we have investigated the phylogeny and function of intracellular bacterial symbionts inhabiting the trophosome of specimens of Lamellibrachia sp. from the Amon mud volcano, as well as the bacterial assemblages associated with their tube. The dominant intracellular symbiont of Lamellibrachia sp. is a gammaproteobacterium closely related to other sulfide-oxidizing tubeworm symbionts. In vivo uptake experiments show that the tubeworm relies on sulfide for its metabolism, and does not utilize methane. Bacterial communities associated with the tube form biofilms and occur from the anterior to the posterior end of the tube. The diversity of 16S rRNA gene phylotypes includes representatives from the same divisions previously identified from the tube of the vent species Riftia pachyptila , and others commonly found at seeps and vents.     

Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, not to frenulate pogonophorans (Siboglinidae, Annelida)

Siboglinids, previously referred to as pogonophorans, have typically been divided into two groups, frenulates and vestimentiferans. Adults of these marine protostome worms lack a functional gut and harbor endosymbiotic bacteria. Frenulates usually live in deep, sedimented reducing environments, and vestimentiferans inhabit hydrothermal vents and sulfide-rich hydrocarbon seeps. Taxonomic literature has often treated frenulates and vestimentiferans as sister taxa. Sclerolinum has traditionally been thought to be a basal siboglinid that was originally regarded as a frenulate and later as a third lineage of siboglinids, Monilifera. Evidence from the 18S nuclear rDNA gene and the 16S mitochondrial rDNA gene presented here shows that Sclerolinum is the sister clade to vestimentiferans although it lacks the characteristic morphology (i.e., a vestimentum). The rDNA data confirm the contention that Sclerolinum is different from frenulates, and further supports the idea that siboglinid evolution has been driven by a trend toward increased habitat specialization. The evidence now available indicates that vestimentiferans lack the molecular diversity expected of a group that has been argued to have Silurian or possibly Cambrian origins.     

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

The members of the genus Heterixalus constitute one of the endemic frog radiations in Madagascar. Here we present a complete species-level phylogeny based on DNA sequences (4876 base pairs) of three nuclear and four mitochondrial markers to clarify the phylogenetic relationships among and within all known species of this genus, as well as the phylogenetic position of the monospecific Seychellean Tachycnemis seychellensis. Although the performance to resolve supported clades of Heterixalus species differed among the investigated gene fragments when analyzed separately, we could identify five well-supported species groups within Heterixalus in the combined analysis of all gene fragments. Our data strongly support a Heterixalus-Tachycnemis clade, and indicate the probable monophyly of Heterixalus placed sister to Tachycnemis. However, the diversification of these lineages may have happened in a short interval of time, leading to an unstable placement of Tachycnemis in the single-gene fragment phylogenies. Referring to the hitherto existing classification of Heterixalus, which is predominantly based on chromatic and bioacoustic characters, we examined the relative performance of these data sets relative to our molecular phylogeny. A Bayesian tree reconstructed with a bioacoustic data set yielded a higher resemblance to the molecular phylogeny than a tree constructed using a chromatic data set, which supports the importance of bioacoustic characters for systematic analyses of these anurans.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

Molecular phylogenetic analysis of Commiphora (Burseraceae) yields insight on the evolution and historical biogeography of an "impossible" genus

Expansion of the arid zone of sub-Saharan tropical Africa during the Miocene is posited as a significant contributing factor in the evolution of contemporary African flora. Nevertheless, few molecular phylogenetic studies have tested this hypothesis using reconstructed historical biogeographies of plants within this zone. Here, we present a molecular phylogeny of Commiphora, a predominantly tropical African, arid-adapted tree genus, in order to test the monophyly of its taxonomic sections and identify clades that will help direct future study of this species-rich and geographically widespread taxon. We then use multiple fossil calibrations of Commiphora phylogeny to determine the timing of well-supported diversification events within the genus and interpret these age estimates to determine the relative contribution of vicariance and dispersal in the expansion of Commiphora's geographic range. We find that Commiphora is sister to Vietnamese Bursera tonkinensis and that its crown group radiation corresponds with the onset of the Miocene.     

A modern approach to rotiferan phylogeny: combining morphological and molecular data

The phylogeny of selected members of the phylum Rotifera is examined based on analyses under parsimony direct optimization and Bayesian inference of phylogeny. Species of the higher metazoan lineages Acanthocephala, Micrognathozoa, Cycliophora, and potential outgroups are included to test rotiferan monophyly. The data include 74 morphological characters combined with DNA sequence data from four molecular loci, including the nuclear 18S rRNA, 28S rRNA, histone H3, and the mitochondrial cytochrome c oxidase subunit I. The combined molecular and total evidence analyses support the inclusion of Acanthocephala as a rotiferan ingroup, but do not support the inclusion of Micrognathozoa and Cycliophora. Within Rotifera, the monophyletic Monogononta is sister group to a clade consisting of Acanthocephala, Seisonidea, and Bdelloidea-for which we propose the name Hemirotifera. We also formally propose the inclusion of Acanthocephala within Rotifera, but maintaining the name Rotifera for the new expanded phylum. Within Monogononta, Gnesiotrocha and Ploima are also supported by the data. The relationships within Ploima remain unstable to parameter variation or to the method of phylogeny reconstruction and poorly supported, and the analyses showed that monophyly was questionable for the families Dicranophoridae, Notommatidae, and Brachionidae, and for the genus Proales. Otherwise, monophyly was generally supported for the represented ploimid families and genera.     

Biogeography and speciation patterns of the golden orb spider genus Nephila (Araneae: Nephilidae) in Asia

The molecular phylogeny of the globally distributed golden orb spider genus Nephila (Nephilidae) was reconstructed to infer its speciation history, with a focus on SE Asian/W Pacific species. Five Asian, two Australian, four African, and one American species were included in the phylogenetic analyses. Other species in Nephilidae, Araneidae, and Tetragnathidae were included to assess their relationships with the genus Nephila, and one species from Uloboridae was used as the outgroup. Phylogenetic trees were reconstructed from one nuclear (18S) and two mitochondrial (COI and 16S) markers. Our molecular phylogeny shows that the widely distributed Asian/Australian species, N. pilipes, and an African species, N. constricta, form a clade that is sister to all other Nephila species. Nested in this Nephila clade are one clade with tropical and subtropical/temperate Asian/Australian species, and the other containing African and American species. The estimated divergence times suggest that diversification events within Nephila occurred during mid-Miocene to Pliocene (16 Mya-2 Mya), and these time periods were characterized by cyclic global warming/cooling events. According to Dispersal and Vicariance Analysis (DIVA), the ancestral range of the Asian/Australian clade was tropical Asia, and the ancestral range of the genus Nephila was either tropical Asia or Africa. We conclude that the speciation of the Asian/Australian Nephila species was driven by Neogene global cyclic climate changes. However, further population level studies comparing diversification patterns of sister species are needed to determine the mode of speciation of these species.     

Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea)

Siboglinid tubeworms do not have a mouth or gut and live in obligate associations with bacterial endosymbionts. Little is currently known about the phylogeny of frenulate and moniliferan siboglinids and their symbionts. In this study, we investigated the symbioses of two co-occurring siboglinid species from a methane emitting mud volcano in the Arctic Ocean (Haakon Mosby Mud Volcano, HMMV): Oligobrachia haakonmosbiensis (Frenulata) and Sclerolinum contortum (Monilifera). Comparative sequence analysis of the host-specific 18S and the symbiont-specific 16S rRNA genes of S. contortum showed that the close phylogenetic relationship of this host to vestimentiferan siboglinids was mirrored in the close relationship of its symbionts to the sulfur-oxidizing gammaproteobacterial symbionts of vestimentiferans. A similar congruence between host and symbiont phylogeny was observed in O. haakonmosbiensis: both this host and its symbionts were most closely related to the frenulate siboglinid O. mashikoi and its gammaproteobacterial symbiont. The symbiont sequences from O. haakonmosbiensis and O. mashikoi formed a clade unaffiliated with known methane- or sulfur-oxidizing bacteria. Fluorescence in situ hybridization indicated that the dominant bacterial phylotypes originated from endosymbionts residing inside the host trophosome. In both S. contortum and O. haakonmosbiensis, characteristic genes for autotrophy (cbbLM) and sulfur oxidation (aprA) were present, while genes diagnostic for methanotrophy were not detected. The molecular data suggest that both HMMV tubeworm species harbour chemoautotrophic sulfur-oxidizing symbionts. In S. contortum, average stable carbon isotope values of fatty acids and cholesterol of -43 per thousand were highly negative for a sulfur oxidizing symbiosis, but can be explained by a (13)C-depleted CO(2) source at HMMV. In O. haakonmosbiensis, stable carbon isotope values of fatty acids and cholesterol of -70 per thousand are difficult to reconcile with our current knowledge of isotope signatures for chemoautotrophic processes.     

Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2

Sequences from the mitochondrial cytochrome oxidase subunit 2 gene (cox2) were determined for 14 species from the family Ceratopogonidae, representing 12 genera and all five subfamilies, along with six representatives of other nematoceran families. The purpose was to develop a molecular phylogeny of the Ceratopogonidae, and interpret the phylogenetic position of the family within the infraorder Culicomorpha. These taxa have been analysed using cladistic methodology which, in combination with an excellent fossil record, provides a well established morphological phylogeny. Sequence analysis of cox2 revealed a high degree of sequence divergence among the species, reflecting in part the antiquity of the family, but also a significant acceleration of sequence evolution in the ceratopogonids compared to other nematoceran Diptera. Phylogenetic reconstruction by neighbor-joining and maximum parsimony gave strong support for an early separation of an ancient lineage that includes the two genera, Austroconops and Leptoconops, from the remainder of the family. The results support the existence of a clade that includes two subfamilies, Dasyheleinae and Forcipomyiinae, and this clade appears as sister to the remaining subfamily, Ceratopogoninae. The molecular phylogeny also supports monophyly of the Ceratopogonidae, and either a sister or paraphyletic relationship of this family with the Chironomidae.     

Relationships within Siphini (Hemiptera,Aphidoidea: Chaitophorinae) in light of molecular and morphological research

The aim of this paper was to further explore the phylogeny of Siphini by analysing molecular data (two mitochondrial genes and two nuclear markers), together with morphological (29) and ecological (two) characters, for comprehensive analyses concerning the evolution of Siphini, relationships within the tribe, and between Siphini and other Chaitophorinae. Nine Siphini species, which represent all the genera of this tribe, as well as 12 out‐group species (mainly Chaitophorini representatives of the genera Chaitophorus and Periphyllus), were used in the analyses. Molecular phylogenetic trees were reconstructed by the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. The cladistic analysis was performed using nona . The monophyly of Siphini was confirmed. Species belonging to subgenera Sipha and Rungsia were clustered together, and this clade was a sister with reference to a clade including the genera Atheroides and Chaetosiphella. Monophyly of Atheroides was confirmed by the molecular data; however, in cladistic analysis Atheroides seemed to be paraphyletic because Atheroides hirtellus was placed as sister to Atheroides serrulatus and Chaetosiphella. The monotypic genera Caricosipha and Laingia formed separate lineages, and Laingia was sister to all other Siphini. Chaitophorini was not retrieved by the molecular and combined data: Periphyllus was sister to a clade containing Chaitophorus and Siphini.     

Tree of life for the genera of Chinese vascular plants

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13?695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.